Genome-wide Analysis Reveals High Genomic Diversity and Panmixia in Bay Pipefish ( Syngnathus leptorhynchus ) from Coos Bay, Oregon

ABSTRACT The over 300 species of fishes in the charismatic family Syngnathidae (seahorses, pipefish, pipehorses, and seadragons) exhibit remarkable morphological and reproductive adaptations. Most syngnathid species inhabit shallow coastal regions where they are vulnerable to human activities, including habitat degradation and collection for use in traditional medicine and the aquarium trade. A gap remains in our understanding of within-species genetic diversity and population structure for most of the species in this family—information that is crucial for establishing baselines to detect future human-driven changes. Here, we investigate fine-scale population structure and genomic diversity in the bay pipefish ( Syngnathus leptorhynchus ), one of the relatively few temperate lineages within the Syngnathidae. Bay pipefish are habitat specialists that are closely associated with eelgrass ( Zostera marina ) along the Pacific coast of North America. Due to the patchy and changing nature of eelgrass habitat, bay pipefish provide an instructive case for using population genomics to explore patterns of connectivity in a dynamic coastal environment. We sampled 116 individuals from two locations separated by approximately 17 km in the Coos Bay estuary (Oregon, USA) and used restriction site-associated DNA sequencing (RAD-seq) to discover high and consistent genetic diversity at both sampling locations, with no indication of inbreeding. Genome-wide patterns of genetic variation showed minimal differentiation between the sampling sites, with levels of divergence indistinguishable from those expected under random sampling. Linkage disequilibrium was low and declined rapidly, and estimates of effective population size indicate a large, well-connected population within Coos Bay. These results establish a crucial genomic baseline for understanding how bay pipefish populations may respond to ongoing changes in their eelgrass habitat and offer a genomic framework for conservation and comparative studies across the Syngnathidae.